


River's Big Secret Has Been Discovered

by HisBespokePsychopath



Category: Doctor Who
Language: English
Status: In-Progress
Published: 2014-06-28
Updated: 2014-07-12
Packaged: 2018-02-06 14:53:47
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 5,540
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1861986
Author URL: https://archiveofourown.org/users/HisBespokePsychopath/pseuds/HisBespokePsychopath
Summary: <blockquote class="userstuff">
              <p>The Doctor receives a message from a young woman on his psychic paper asking for help. Even though he shows up seven years late the surprise of the big secret his wife has left him will turn his life upside down. River has kept many secrets from her husband but he never thought she would hide his own child from him.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> Im sorry if this is a little bad. This is my first try. I will be adding more to this. Thank you!

It has been almost a year in human years since her marriage to the Doctor. It seems like it has been forever since he has found out who she really is. Melody Pond. Everything happens for a reason and she has to believe that this pregnancy is one of those things. Her water broke about an hour ago and breaking out of Stormcage was rather difficult without the use of her vortex manipulator. She was now giving birth to her and the Doctor's first and probably only child in her parents home. She made her parents promise to help her find a home for the baby.  
"Why aren't you keeping her?" Rory asked with complete disbelief.  
"I don't want to give Kavarian the chance to take my baby and use her against her own father." She refused to give the Silence another weapon to use against her beloved husband. Especially his own daughter.  
"Speaking of where is he? It is the Doctor isn't it?"  
"Of course it is! You stupid face!" Amy squeals.  
"He doesn't know." River replys.  
"River! Why haven't you told him!" Demands Rory.  
"Father, it will give him a big head and he will not think of the dangers. He will one day know but until then this is whats best for him."  
Fifteen hours later lay little Aaelee Rose Pond in her mothers arms. River can only stare in aw as silent tears run down her cheeks. She doesn't want to give her up but she knows the future that awaits her and the future that will await her daughter if she keeps her. It didn't take long for Amy to find a good family. A cousin of Rory's who could never have a child. They took the child and understood who she was. They agreed that River could visit as much as she wanted and with that and one last kiss to her daughters tiny little head they left.

***********

April 21, 2007

Aaelee is confused. She remembers riding with her parents to get her stuff for her graduation. Then pain. No wait there was an accident. If she really focused she could remember some things. Such as the sound of twisting metal, screeching tires, and calling out for help to her favorite childhood superhero. Which now seemed kind of dumb the man in the bow tie and fez wasn't real. He was just from a story book her parents had given her from a family member on her dads side. A nurse walks in to check her vitals and interrupts her thoughts.  
"Where are my parents? Are they okay?" She asks a little frantically.  
"Sweetie I'm so sorry but they didn't make it. The wreck was so bad we are amazed you made it out alive."  
"What! No! This can't be happening!" She sobs into her hands.  
"We will help you get through this. I am so sorry" The nurse hugs her close and tries to help the poor girl whose world just turned upside down.

***********

June 28, 2014

"We made it girly! College graduation! I never thought it would come but its here!" Screamed Aaelee's best friend Natalie.  
"Nat you might be done but I am coming back in a year or so. I am determined to get my doctorate." Replied Aaelee.  
"Yes, of course, you wont stop till you have that doctor in front of your name."  
Aaelee continues talking to her friend for a time and accepting congratulations from friends and their families.  
"Your family would be so proud of you Aaelee." It was her nurse from all those years ago when she had lost her parents. She said she was going to help her get through her loss and she had and still was.  
Aaelee was about to tell her thank you for everything but saw someone out of the corner of her eye that made her look more closely. A man dressed so ridiculously but the thing that had caught her eye was the bow tie and fez that he was wearing.  
"It can't be. He's not real. He was just in a story book when I was a young girl," she whispers to herself forgetting the nurse was there.  
"Aaelee are you alright?"  
"What? Oh yes. Thank you so much for everything but I need to go get ready for an interview. I will talk with you again soon. Goodbye!"  
Aaelee runs after the man which ends up only confirming he was the man from her book. The gangly, leggy man in the bow tie and fez was standing against a big blue police box messing with a piece of something and talking to himself. It was him. It was the Doctor!  
"Doctor!" Aaelee yells breaking his concentration and ranting.  
"I'm sorry have we met before?"  
"Well not really but a family member gave me a book when I was younger and it was about the Doctor, his crazy wife River Song, and River's parents the Ponds. How are you real?"  
"I imagine the same way you are. Where did this family member get this book?"  
"I don't know. I just remember my cousin bringing it to my parents for me for my birthday. It became my favorite story. I loved River but I always knew the Doctor was my hero."  
The Doctor smiled until he heard gun shots being fired. He started looking for the source of the shots and went to grab Aaelee to keep her from getting hurt but she wasn't there anymore. She was on the ground with blood slowly turning her white graduation gown red. The Doctor picks her up and takes her to the med bay in the Tardis. He couldn't let her die before he found out who she was and where the book came from. He was running around grabbing things to help her until he saw something that had him dumbfounded. She was glowing. No not glowing regenerating! How is this possible he thinks. Then bam shes laying there with another face.  
"Who are you?" The Doctor demands not trusting anything or anyone right now.  
"My name is Aaelee. What just happend?"  
"You were shot."  
"And I changed again didn't I?"  
"Changed?"  
"Yeah when I was eighteen I was in an accident with my parents. They died but I changed. I became someone else but with the same memories."  
"It's called regeneration. You are a time lord well lady. How though I am the last of my kind."  
" I was born this way my mother said I was just gifted. She said she knew that I was special the moment my real mother placed me in her arms."  
"You were adopted?"  
"Yes."  
"Who are your real parents?"  
"I don't know. All I know was that my real mother could not keep me."  
"Do you still have that book?"  
"Yes it's in my dorm."  
She then realizes she not at her school anymore. "Oh My God! Am I in the bigger on the inside Tardis!"  
"Yes. Hold tight we're going to to get that book."  
With a shift and a couple of noises the Tardis lands and he walks to the door. She walks to the door and is astonished that they are in her dorm. She walks over to the trunk at the end of her bed and gets out the book and hands it to him. He refiles through it looking for something and notices that the last page is a little thicker than it should be. I tears it out.  
"Hey! What are you doing!"  
He pulls out a small chip and says, "Someone knew I would find you and they left this. Time to find out who."  
"How come I never noticed that?"  
"It was hidden so you wouldn't find it but I knew what to look for."  
Confused she follows him back into the Tardis. He puts the chip in a small compartment and with a few dings a video pops to life. He falters at the picture of the woman.  
"Hello sweetie. I knew you would find her eventually. This is Aaelee Rose Pond. Your daughter. I know that you must be angry but please understand. I did what was best for her. You know that Madam Kavarian would come after her so I hid her. Even though I knew that you would fight to keep us together and safe. I'm sorry my love but you have her now. Please understand that I didn't do this to hurt you. I wanted to keep our baby safe. I'm sorry."  
The screen went blank again and the Doctor looked as if he had just been punched in the stomach. His mind raced. He had a daughter and his wife had kept her from him.  
"Wait a minute! You mean to tell me that that book isn't really a story book but a journal of past adventures had by my family! No wait! You're my dad!"  
Aaelees mind began turning and she was in shock. The Doctor was her father! River was her mother! Rory and Amy were her grandparents!  
"I must be dreaming! This can't be real."  
"Well lets find out if you really are my daughter. I will do a DNA test here on the Tardis and we will know for sure if you are or are not my daughter."  
He pokes her finger and then his and does the DNA test. They wait a few minutes and find out that Aaelee is the Doctors daughter. He can't believe it. River has been gone for twenty two years human years and even though she regenerated she still looked like her mother well mostly because of the space hair. How he missed River, missed those curls. She had his eyes though. She was beautiful and she was his. He had so much to do and say. So much to teach her. Where to start?  
"Well we have all of time and space. Where do you want to start."


	2. Chapter 2

**Summary for the Chapter:**

> Aaelee finds out that she has known her mother all along and wants to see her again. The doctor tries to find River only to get another surprise.

"When you say all of time and space do you mean ALL of Time and space?"  
"Well yes and no. I can't cross my timeline or yours for that matter. Might get messy."  
"I wanna see my mother."  
The Doctor's face drops from a smile to a frown in no time. How to tell her not only are her adoptive parents dead but so is her birth mother.  
"Why such a long face? Did you and mom get a divorce or something? What the hell am I even saying, I don't even know if you were married."  
"We can't see her."  
"Why?"  
"She's...gone."  
"Gone how? Did she leave you?"  
"No dear she died. In human years I would say about twenty something years."  
That made her drop into the seat next to her. All of her family was dead except the man standing in front of her. Why?  
"So I can never see her? Ever? Even though this thing is a time machine?"  
"Believe me I have tried to find a past her. It is important for you to know that I loved your mother. More than anything. She died saving me from myself. Well after she tried to kill me. Good old River Song. My bespoke psychopath."  
As she watched him speak of her mother she could see a single silent tear run down his face. Even though he smiled.  
"I have been working on something that would let her live in the Tardis but haven't got it quite ready yet."  
"Is she a ghost or something?"  
"You might say that. I saved her mind if you will to a database in the largest library in the universe. At the time I didn't even know her but she knew my name so I knew that she would mean something very special to my future self and couldn't let her just die for me. Plus I don't like endings. I want to find a way to hack into said database so that I can bring her into the Tardis and have her with me always."  
"Would I be able to interact with her? Like if she were alive?"  
"Yes. She would be like you said a ghost but still have an intact mind so that she would be able to interact a little more than a ghost would."  
"I would really like that. Do you have a picture of her?"  
"Of course she was my wife but you saw her in the video."  
"Sorry but I wasn't really watching mostly staring into space dumbfounded that I was on the Tardis."  
"Yeah that seems to happen a lot. Hang on I'll pull up a picture." He began flipping switches and saying a few choice words in a language she didn't know until he finally gave up and went below to a trunk and pulled out a picture of the two of them in what looked like Renaissance clothing. She gasped.  
"What is it?"  
"She was my nurse! After my parents died! She was at my college graduation when I changed. I saw you and went to see if it was really you and well here we are but oh my gosh I knew my mom. How is that possible?!"  
"Oh River you bad girl." He said this more to himself than to her with a smile. "She has been checking on you your whole life from the shadows."  
"But how you said she died when I was like what two, three years old."  
"River knew that she didn't have forever and after having you she must have wanted to know that you were okay. She used her vortex manipulator to jump from time to time. Like to give your family the book to when they died so that she could be there for you and then to see your big day."  
"A vortex mawhata?"  
"A vortex manipulator looks like a watch but is a time machine of sorts. She used it to jump from time to time to find you. She must have upgraded it so that she could always find you. So you might be able to find her after all!" He jumps up and starts running around clearly ecstatic. He was about to prick her finger to use as a homing beacon to find River until he heard a sound he had not heard in ages. A sound he dare not think about in fear of overwhelming pain.  
"Mom?"  
The Doctor fell to his knees without turning around. "River." One word. The only word that could leave him.  
"Hello sweetie."  
He jumped to his feet and ran for her. Swinging her up in his arms he cried, "I thought I would never see you again. I just wanted one more night, day, even five more minutes."  
"So I did die. Nice to know. At least I got to watch over our baby until you found her." Looking over at Aaelee she continued, "You must have so many questions."  
"Yes."  
"Well sweetie ask away I don't have much time."  
"River what time are you from," the Doctor asks.  
"I'm about to leave for our date to Derillium. You argued with me, do you remember?" He ran over to River and kissed her hard and then answered her.  
"Yes you said you had some business to attend before our date and I just wanted you to stay with me. I must say if you had just told me you were going to see me I wouldn't have fought you."  
"Spoilers." She hugged him tight and looked back at Aaelee.  
"Can I call you mom? I mean would you want me to call you mom or just by your name?"  
"Oh my dearest Aaelee. I would love to finally hear you call me mom. I love you so very much and it killed me to leave you."  
"Okay first things first. Why Aaelee?"  
River laughed at this as did the Doctor before he straightened up and looked as if he were missing something. River slapped his chest.  
"For your grandmother. Amelia, Amy. She was Scottish and so is Aaelee not to mention it is so very close to Amy. I wanted to name you after my mother because she was such a strong woman and I wanted you to be as well. I hoped you would be like her. Strong. I could not name you Amelia for fear you would be found."  
"Found? Found by who? Not dad right?"  
"No not your father. Had he known you were alive he would have taken you be damned how I felt. You are his baby. No there was a woman who,"  
"Madam Kavarian? From the book? The one that stole baby River."  
"So you got the book. I hoped you would like it."  
"I love it."  
"And I love you but I'm afraid I have to leave. I have to get back to the past Doctor before he starts looking for me. I love you both so very much."  
She gave Aaelee a hug and kissed her on the head like she did when she was a baby and turned to the Doctor.  
"I'm sorry my love."  
"Please stay. I can't lose you again." Aaelee looked at her father and watched as he broke down like a child. The love he held for her mother was breathtaking and sad. She could feel herself begin to shake as tears began to fall down her face. She grabbed his hand to let him know it was okay. He looked at her and smiled sadly.  
"Aaelee you wont be seeing me again and I am so sorry but I feel as if my time is up. I know your father will have something up his sleeve to save me somehow he always does. Always catches me when I fall and always forgives me. I love you my sweet little girl and never give up." She then turned to the doctor and sighed, "My love, my dearest love. Teach her well. Love her for me and make sure she gets her doctorate. I love you." With a kiss and a sad goodbye she pressed a few buttons on her vortex manipulator and was gone. Aaelee turned to her father who kept on silently crying and hugged him.  
"We will find a way to get her back here. I promise. We will be a family again." She said. The Doctor looked down at his little girl. She wasn't very little but she would always be his little girl. He had only known her a few hours and he had already fallen in love with her. She was now his life and he would never change that. She was what little of his River he had left.  
"What doctorate was your mother talking about?"  
"Archaeology."  
"Oh you are your mothers child. She only wants you to get it to mess with me. Archaeology. Bunch of crap if you ask me. You don't happen to like guns do you?"  
"Who doesn't like a gun every now and again?"  
"Oh I am doomed!" He shouted this as he walked across the control room of the Tardis. "You said she only wanted me to get my doctorate to mess with you. What did you mean?" "She was Dr. River Song, Archaeology. Now lets get to finding a way to bring your mother back to us!"


	3. Chapter 3

**Summary for the Chapter:**

> After finding out the doctor has a daughter he and said daughter seek out on an adventure to retrieve River from the library!

It's been a couple weeks since the Doctor and Aaelee have started their search for a way to get River back but have been having a hard time finding a way. The Doctor has been running around like the mad man he is and scratching at his head in thought while Aaelee has been staying in the library trying to learn as much as possible about her race, the great time lords and ladies. Don't think she hasn't been reading up on the villains in her fathers life either because if she ever has to she wants to be ready to fight them side by side with her father. The Doctor has always been her hero but learning that he is her father amazes her and makes her feel like the luckiest girl in the universe. He's kind and loving but she knows that he has a dark side. Instead of fearing it though she loves him even more because he is the man he is because of it. Through every regeneration he changes but he's always the same. She doesn't understand how he hasn't become a monster yet with all the loss and sadness not to mention the weight of the universe on his shoulders. He has seen so much, lived through so much, and lost so much. Regardless of it all he puts it aside and continues saving the lives of millions and continues to love. She loves him so much already in such a short time. She's curious as to what he is, who he is, so she looks for him in the library. She finally finds a book covered in dust and cracks it open.  
Theres information on the race but nothing on the Doctor. She assumes that the torn out pages are about him and heaves a sigh as she closes the book. Will she ever truly figure this man out.  
"Aaelee!"  
"Yes dad? In here!"  
"Ah there you are. I have brought food. Figured you might be in here and hungry so I popped out and got you something."  
"Oh thanks. How long have I been in here?"  
"About five hours or so. I don't know never really paid attention to time. You know with a time machine and all never really mattered much."  
"I guess time really wouldn't matter if you had control of it. What are we doing today?"  
"Well it's wednesday so we need to pick up Clara and then well who knows." He claps his hands together and acts rather excited.  
"Do you like her? Not any of my business but you look really excited and well..."  
"I like her yes but as a friend, a companion, but no worries. No one will ever replace your mother. She's my impossible girl and I wouldn't be here if not for her. She has been there and pulled me out of a lot. Saved your old dads butt quite a few times. I hope you like her."  
She nods and he leaves her to her food. She knows now that her father doesn't love this women but it still bothers her that he can travel around with all these female companions that aren't her mother. She shakes it off and finishes eating before she hears a womens voice.  
"Your what?! You have a daughter?!" It's Clara  
"Shhh Clara, yes I have a daughter, hasn't been bad, actually kind of nice to have family. Plus she doesn't drive me crazy like her mother!"  
"Give it time. She is the daughter of River Song and you of course. Where is she I want to meet her?!"  
"She's in the library. Be good to her I want you two to be close. She could probably use a friend right now."  
Aaelee decides to make her entrance with a deep breath she calls out to the Doctor. "Dad?" Clara smiles.  
"Hello dear. Done reading?"  
"Yep, had to stretch the old legs for a bit." He walks over to her and grabs her hand pulling her to Clara.  
"Clara, this is my daughter Aaelee. Aaelee, Clara."  
"Hi Clara. It's nice to meet you."  
"Same to you. Wow you look so much like your mother."  
"She didn't a few weeks ago. Looked oddly like me. Rather strange to have someone who looks like you. I think,"  
Clara cut him off and lead Aaelee to sit down so that they could have a chat. "So tell me about you." Clara says.  
"Well I was adopted by well I guess it would have been my cousins but never knew they were my cousins. They died when I was a teenager about to graduate high school in a car crash which triggered my first regeneration. Then I lived on my own for a while until I went to college and got my bachelors degree in archaeology which is the day I met dad." She looks up at the Doctor and smiles and he gets lost in her eyes thinking of everything she had been through. River did well in naming her. She was a strong person, just like his Amelia Pond.  
"I was actually shot at my college graduation and regenerated again. Thats when I thought dad was going to tear my head off until he found out who I really was. Which might I add was strange even for me."  
"So you have regenerated and still look like your parents? How does that work?" Clara asks.  
The Doctor answers this question, "In some cases, rare cases I might add, if the bond between the mother and father is extremely strong while the child is in the womb the child is sometimes gifted with eternal love which forever gives the child the resemblance of the parents. Very rare. I didn't realize that River and my bond had run so deeply."  
Aaelee sees how hurt talking about her mother made him. He really loved her and she now understood that all the companions were simply that nothing more.  
The Doctor spins around after a second with his face wiped of emotion. "Right then. Lets get busy lots to do, places to see. I'm sorry Clara but I made a pact to get my wife back for my daughter, and well for me as well because well I hate endings. So any plans you have will have to wait."  
"Of course! Where do we start? Are we going to the library?"  
"No, well not at the moment I need to see an old friend first. Well no nevermind. Ignore everything I said." Clara laughs as he walks away.  
"Dad I have been working on something you might want to see."  
Aaelee pulls out a notebook and opens it to a million doodles and notes. "After everything you have told me about where moms stuck I began thinking of ways to bring her on to the Tardis as a ghost person."  
The Doctor looks at what Aaelee has shown him. It was a device that could be attached to his sonic screwdriver that would act as a memory chip that would safely transport River back to his sonic screwdriver. The next thing was a device that could be attached to the Tardis. River would be able to roam freely around the Tardis and interact with all of them.  
He looked at his daughter mind racing at the thought of how to build the devices. He grabbed her in a hug and said, "Takes after me! Smart as a tack."  
Aaelee hugs him tight before letting go to hug Clara. Clara is shocked but hugs her back.  
"I need sleep. I think that I have been up longer than five hours dad. I'll go nap and leave you two to whatever you do when I wasn't around."  
"Ok dear," he mumbles as he starts to tinker with some odd spare parts.  
Aaelee walks to her room and lays down. About an hour later she wakes to a bang and a shudder of the Tardis.  
"No! No! No!

"What's going on?!" Clara yells as the Doctor runs around flipping switches and pushing buttons.  
"Daleks! And if I'm right they are trying to shoot us down!"  
"Dad!" Aaelee yells.  
"It's okay dear just go sit in your room. I'll come get you when its over."  
"No! I wanna help!"  
"Okay come here and listen carefully." Aaelee ran to her fathers side and did as he said.  
"Flip this switch when I say and then pull the wibbly lever! Only when I say. Okay?"  
"Yes."  
After about an hour they were free and once again flying through space. Aaelee decided she was bored and went to her room and turned on some music. She laid down on her bed and began to daydream about what it would be like to have both of her real parents around. Would they fight like all old married couples or would they act like the perfect spacey couple? She couldn't wait to have them both in her life and live like a semi normal person. You know like a normal alien child who lived on a time machine and was getting her doctorate in archaeology.  
"Aaelee! Could you turn that down?! I can hear it all through the Tardis!" She laughed her father was such an old man. She gets up and turns off the music altogether and heads to the control room of the Tardis. She can tell they've landed somewhere.  
"Where are we?"  
"Akhaten! It's lovely and we need to get a few parts for your plan daughter."  
"It's going to be a little weird since the last time we were here we almost ended the planet." Clara mumbled.  
"You almost ended the planet?!" Aaelee's jaw dropped as she asked her father.  
"No! Well yes but it was my mistake and it's still here jeez."  
Aaelee laughed and they left the Tardis. "We need to find a man called Lorn. He's got a part called the sonic memory. Not very creative but it is what it is. It will allow me to save data to my sonic and if I can change it a bit I can save a human conscious to the sonic allowing me to save River. Then we need to find a woman who goes by the name of Randalin. She has a part that I can add to the Tardis that creates a data space within the Tardis so that we can develop a Tardis within the Tardis. By doing so we can have River living in the Tardis data space and project her in the actual Tardis so that she can interact with us all."  
Aaelee stared at her father in disbelief. "There are people out there that actually make these things?"  
"Yes."  
"Well then lets not keep mother waiting!" Aaelee grabbed the Doctors and Claras hands and dragged them forward.  
"Other way!" Yelled the Doctor. Aaelee spun around and continued.  
It didn't take long for them to find Lorn but Aaelee was shocked that he was remotely what she thought he would be. He looked like a pig but spoke as a human and stood like a human as well.  
"How much for the sonic memory," asks the Doctor.  
"A most cherished item will suffice."  
The Doctor looked at Clara and then Aaelee.

"Don't look at me I used mine last time we were here," Clara said.  
Aaelee reaches in the bag she was carrying , the one she always carries. She reached in and brought out her childhood book about the Doctor.  
"Aaelee that's your book. Your families book." The Doctor looked at Aaelee as if he were in pain.  
"It's okay dad. I have you and I will have mom, I don't need the book if I have the real thing right? Plus mom could always have another one made for me." She smiled at him and handed Lorn the book. He held it like it was very precious and closed his eyes. With a smile he nodded and handed the Doctor the part. The Doctor hugged Aaelee.

As they walked back to the tardis with all of their purchases Aaelee asked the Doctor, "So dad how did you find this place?"  
"Oh I have been here loads of times. With Clara, oh and my granddaughter. Which would be your niece? Right yes niece."  
"I have a niece?! Wait I have a sibling?!  
"Had. I imagine they are all gone now. Of course knowing your mother you probably have other siblings out there she hasn't told me about!"  
"DAD!"  
"Doctor that wasn't very nice. She hid Aaelee for a good reason so knock it off." Clara was glaring at the Doctor as she said this.  
"Right sorry. Im still a little mad at her. She should have told me."  
The Doctor walked over to the console and started messing with the bits and pieces that they had bought and Aaelee asked, "Dad you said that you went their with my niece, did she travel with you?"  
"For a while yes. Then she fell in love with a human and stayed behind."

Clara seemed flabbergasted that the Doctor was talking about things that he would never talk to her about. It kind of hurt but Aaelee was his daughter. She never saw him with anyone other than her and a select few not even River. He was hers but now she would just have to get used to sharing him. It was his daughter after all. Clara wanted to be friends with Aaelee. Why not they were about the same age and had one big thing in common. The Doctor. Her train of thought was broken at the sound of the Doctor yelling, "AH HAH."  
She turned her attention back to reality to see Aaelee jumping up and down and the Doctor grinning that stupid boyish grin while staring at his wife. Clara blinked. River Song was on the Tardis!

**Author's Note:**

> I would love any feed back that you might have! Also if there are any suggestions hit me up and I will hear them and run with them. Thank you for taking the time to read my work!


End file.
